Ribosomal protein L5



Ribosomal protein L5 (RPL5) is one of the 34 proteins which belong to the large 50S subunit of the prokaryotic ribosome or to the ca. 49 proteins in the large 60S subunit of the eukaryotic ribosome. It is known to bind to the 5S RRNA from the large subunit. In the archaea like in Haloarcula marismortui, the L5 is called L5P (RPL5P). The images at the left and at the right correspond to one representative RPL5, i.e. the crystal structure of Ribosomal protein L5 from Thermus thermophilus (2xg0, chain G).

3D Structures of Ribosomal protein L5
Update June 2011

RPL5
1iq4 – RPL5 – Geobacillus stearothermophilus

L5 in 50S subunit+RNA
2xg0, 2xg2, 3kir, 3kit, 3kiw, 3kiy – TtRPL5 in 50S subunit+RNA fragments - Thermus thermophilus

2x9s, 2x9u, 3kni, 3knk, 3knm, 3kno, 2wrj, 2wrl, 2wro, 2wrr, 3hux, 3huz, 2wh2, 2wh4, 2wdi, 2wdj, 2wdl, 2wdn, 1vsp, 2v47, 2v49, 1vsa, 2hgj, 2hgq, 2hgu, 2j01, 2j03, 1yl3, 3mrz, 3ms1, 3i8f, 3i8i, 3i9c, 3i9e, 3f1f, 3f1h, 3d5b, 3d5d, 2b66, 2b9n, 2b9p, 1giy, 2y0v, 2y0x,  2y0z,  2y11,  2y13,  2y15,  2y17,  2y19,  3pyo, 3pyr,  3pyt,  3pyv -  TtRPL5 in 50S subunit+5S RRNA+23S RRNA

3fin - TtRPL5 in 50S subunit+5S RRNA+23S RRNA – Cryo-EM

2wwq – EcRPL5 in 50S subunit+5S RRNA+23S RRNA+mRNA+P-site tRNA – Escherichia coli

3i1n, 3i1p, 3i1r, 3i1t, 3i20, 3i22, 3e1b, 3e1d, 3df2, 3df4, 2vhn, 2qov, 2qox, 2i2t, 2i2v, 1vs6, 1vs8, 2aw4, 2awb, 3ofd, 3og0, 1vor, 1vou, 1vow,  1voy,  1vp0,  1pnu,  1pny, 3r8s, 3r8t - EcRPL5 in 50S subunit+5S RRNA+23S RRNA

3fik, 2gya, 2gyc, 3bbx, 1p85, 1p86, 3izt, 3izu - EcRPL5 in 50S subunit+5S RRNA+23S RRNA – Cryo-EM

3kcr - EcRPL5 in 50S subunit+5S RRNA+23S RRNA+preprotein translocase

3j01 – EcRPL5 in 50S subunit+5S RRNA+23S RRNA+preprotein translocase – Cryo-EM

2rdo - EcRPL5 in 50S subunit+5S RRNA+23S RRNA+EF-G+RRF – Cryo-EM

3bbo - RPL5 in 50S subunit+5S RRNA+23S RRNA+4.8S RRNA – Cryo-EM – spinach

3iy9 – RPL5 in 50S subunit – Leishmania taretolae

2zjq, 2zjr, 1nkw - DrRPL5 in 50S subunit+5S RRNA+23S RRNA – Deinococcus radiodurans

1kqs, 1qvg - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+CCA - Haloarcula marismortui

1jj2, 1ffk, 3cc2, 2qa4, 1s72 - HmRPL5P in 50S subunit+5S RRNA+23S RRNA

3cc7, 3cce, 3ccj, 3ccl, 3ccm, 3ccq, 3ccr, 3ccs, 3ccu, 3ccv - HmRPL5P in 50S subunit+5S RRNA+23S RRNA (mutant)

1vq4, 1vq5, 1vq7, 1vql, 1vqm, 1vqp - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+transition state analog

1vq6, 1vqk, 1vqn - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+ c-hpmn+CCA-Phe-caproic acid-biotin

1vqo - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+ CCPMN

1yhq, 1yi2, 1yij, 1yjn, 1yjw - HmRPL5P in 50S subunit+5S RRNA+23S RRNA (mutant)+antibiotic

1yj9 - HmRPL5P in 50S subunit (L22 mutant)+5S RRNA+23S RRNA

1qvf - HmRPL5P in 50S subunit+5S RRNA+23S RRNA + deacylated tRNA minihelix

1q86 - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+CCA-Phe-caproic acid-biotin

L5 in 50S subunit + antibiotics
3dll, 2zjp, 3cf5, 1xbp, 1sm1, 1nwx, 1nwy, 3pio, 3pip - DrRPL5 in 50S subunit+5S RRNA+23S RRNA+antibiotic

3oh5, 3oh7, 3ohj, 3ohk, 3ohz, 3oi1, 3oi3, 3oi5 – TtRPL5 in 50S subunit+5S RRNA+23S RRNA+antibiotic

2qam, 2qao, 2qoz, 2qp1, 2qba, 2qbc, 3ofc, 3ofz, 3ofq, 3ofr, 1vt2, 3orb, 3oas, 3oat - EcRPL5 in 50S subunit+5S RRNA+23S RRNA+antibiotic

1k73, 1kc8, 1k8a, 1k9m, 1kd1, 1m1k, 3i55, 3i56, 3g4s, 3g6e, 3g71, 2qex, 3cpw, 3cc4, 3cd6, 2otj, 2otl, 1yit, 1q7y, 1q81, 1q82, 1n8r, 1nji, 3cxc - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+antibiotics - Halobacterium marismortui

1m90, 3cma, 3cme, 1vq8, 1vq9 - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+ sparsomycin+CCA-Phe-caproic acid-biotin

L5 in 60S subunit
3jyw - RPL5 in 60S subunit – Thermomyces lanuginosus – Cryo-EM

3izr - RPL5 in 60S subunit – wheat – Cryo-EM

1s1i - yRPL5 in 40S ribosomal subunit+18S RRNA+elongation factor 2 – Cryo-EM – yeast

3o58, 3o5h – yRPL5 in 60S subunit+25S RRNA+5SRRNA+5.8RRNA

L5 in large + small ribosomal subunit
1ml5 - EcRPL5 in 50S ribosomal subunit+30S ribosomal subunit+THX+chain release factor 2+P-site tRNA+tRNA Phe+mRNA fragment+23S RRNA+5S RRNA+16S RRNA – EM

2zkr - RPL5 in 60S ribosomal subunit+30S ribosomal subunit+28S RRNA+5.8S RRNA – Cryo-EM - dog

L5 in 50S subunit + ribosome releasing factor (RRF)
2qbe, 2qbg, 2qbi, 2qbk, 2z4l, 2z4n - EcRPL5 in 50S subunit+5S RRNA+23S RRNA+RRF

L5 in 50S subunit + various proteins
2vhm - EcRPL5 in 50S subunit+5S RRNA+23S RRNA+PDF C-terminal helix

2j28 - EcRPL5 in 50S subunit+5S RRNA+23S RRNA+signal recognition particle – Cryo-EM

1w2b - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+trigger factor N-terminal

L5 in part of 50S subunit
3iyx, 3iyy – EcRPL5+RPS13+RPL31 – Cryo-EM

1mji – TtRPL5+5S RRNA